[2026-06-08T08:27:50] Launching Arriba 2.4.0
[2026-06-08T08:27:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:09] Reading chimeric alignments from '659_dES-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12015762)
[2026-06-08T08:36:19] Marking multi-mapping alignments (marked=7719625)
[2026-06-08T08:36:24] Detecting strandedness (reverse)
[2026-06-08T08:36:24] Assigning strands to alignments 
[2026-06-08T08:36:26] Annotating alignments 
[2026-06-08T08:37:02] Filtering duplicates (remaining=8592028)
[2026-06-08T08:37:10] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=8193563)
[2026-06-08T08:37:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8193563)
[2026-06-08T08:37:15] Filtering viral contigs with expression lower than the top 5 (remaining=8193563)
[2026-06-08T08:37:20] Filtering viral contigs with less than 5% coverage (remaining=8193563)
[2026-06-08T08:37:22] Estimating fragment length (mate gap mean=-84.5329, mate gap stddev=27.7016, read length mean=127.293)
[2026-06-08T08:37:22] Filtering read-through fragments with a distance <=10000bp (remaining=7740916)
[2026-06-08T08:37:24] Filtering inconsistently clipped mates (remaining=7580820)
[2026-06-08T08:37:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7386576)
[2026-06-08T08:37:31] Filtering fragments with small insert size (remaining=7385164)
[2026-06-08T08:37:33] Filtering alignments with long gaps (remaining=7385163)
[2026-06-08T08:37:35] Filtering fragments with both mates in the same gene (remaining=7383846)
[2026-06-08T08:37:38] Filtering fusions arising from hairpin structures (remaining=6886160)
[2026-06-08T08:37:40] Filtering reads with a mismatch p-value <=0.01 (remaining=3665213)
[2026-06-08T08:37:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=1606684)
[2026-06-08T08:38:13] Finding fusions and counting supporting reads (total=1195279)
[2026-06-08T08:38:33] Merging adjacent fusion breakpoints (remaining=1183404)
[2026-06-08T08:38:35] Filtering multi-mapping fusions by alignment score and read support (remaining=685506)
[2026-06-08T08:39:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=683150)
[2026-06-08T08:39:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=451093)
[2026-06-08T08:39:22] Filtering fusions with <2 supporting reads (remaining=40574)
[2026-06-08T08:39:23] Filtering fusions with an e-value >=0.3 (remaining=8124)
[2026-06-08T08:39:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8178)
[2026-06-08T08:39:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7983)
[2026-06-08T08:39:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8014)
[2026-06-08T08:39:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7691)
[2026-06-08T08:39:37] Searching for fusions with spliced split reads (remaining=7751)
[2026-06-08T08:39:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=5018)
[2026-06-08T08:39:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4981)
[2026-06-08T08:39:46] Searching for fusions with >=4 spliced events (remaining=6366)
[2026-06-08T08:39:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2884)
[2026-06-08T08:40:04] Filtering fusions with anchors <=23nt (remaining=2379)
[2026-06-08T08:40:05] Filtering end-to-end fusions with low support (remaining=2333)
[2026-06-08T08:40:06] Filtering fusions with no coverage around the breakpoints (remaining=2284)
[2026-06-08T08:40:06] Indexing gene sequences 
[2026-06-08T08:40:16] Filtering genes with >=30% identity (remaining=731)
[2026-06-08T08:40:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=391)
[2026-06-08T08:40:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=291)
[2026-06-08T08:40:28] Searching for additional isoforms (remaining=416)
[2026-06-08T08:40:30] Assigning confidence scores to events 
[2026-06-08T08:40:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:35] Writing fusions to file '659_dES-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:39] Writing discarded fusions to file '659_dES-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:30] Freeing resources
[2026-06-08T08:41:57] Done (elapsed time=00:14:07, CPU time=00:14:06, peak memory=16.8gb)